The Innocence in D.Gray-Man is the Divine Crystal used as a weapon by Exorcists. As such it is obviously harmful to evil beings... but it can just as well be harmful to the good guys. Parasitic type Exorcists (whose weapon is a part of their own body) are stated to have a short life-span due to the sheer amount of energy it consumes. Also, any Exorcist who forgets his mission will be eaten by the Innocence from the inside, and die after turning into an uncontrollable monster that indiscriminately destroys everything around it for several hours. Finally, non-Exorcists cannot stand being exposed to pure Innocence, even if they aren't evil.
In Scrapped Princess, Ginnungagap is the highest known military grade offensive spell, and is so powerful that it must be sanctioned for use, by way of unanimous decision, by the High Council. The attack itself covers a wide area and is devastating enough on its own, but the real threat is resulting shockwave triggered by it. When used, it caused a mega-tsunami that devastated the majority of the continental coast!
As in the scriptures, the Ark of the Covenant in Raiders of the Lost Ark is an inherently dangerous artifact. Indy and Marion only survive the movie because Indy remembers the Bible saying not to look upon the open Ark. Those Wacky Nazis aren't as lucky.
In Indiana Jones and the Last Crusade, the artifact is the Holy Grail, which isn't deadly itself, but has some rather deadly traps protecting it. (Seeing as the Grail can't be taken from the temple and the eternal life it bestows only lasts so long as you stay there, one has to wonder why such traps are necessary.)
Dogma uses the idea that God's voice is fatal to mortals as a plot point. It places Metatron (see Mythology, below) in the role of Mr. Exposition, and is used to destroy the renegade angels.
The Archangel Michael manifesting at full power strains the fabric of reality nearly to the breaking point.
The True Name of God is so potent that, if not kept in two separate pieces, its raw power would destroy entire universes.
If more than one of the Four Great Treasures of Ireland is kept in the same house without proper preparations, the result would "make a nuclear bomb look like a wet firecracker". The spirit of the Spear Liun, whose element is fire, is particularly temperamental: it wants to burn the evil, darkness, and entropy out of things, and it hurts to look at because entropy is bound to some degree into every living thing.
The Book Of Night With Moon, the book (at least as it appears to humans) that defines the operating parameters of the universe, is described as "blindingly bright" (in a psychic sort of way) and most adult wizards fear the idea of being a conduit for such immense power when someone has to read from it to remind the universe how to behave.
In The Dresden Files, Harry receives the Soulfire power from Archangel Uriel, an ostensibly holy ability... which is powered by his own soul. Though according to Bob, this really isn't as big of a deal as Harry thinks it is. The soul is somewhat malleable, and any portion of his soul that he uses up will eventually come back. So long as he doesn't use Soulfire too much in a short amount of time, he'll be fine. If he does, then as Bob put it, "if you subtract five from five..."
The Silmarils were gems of light that burned everything and everybody trying to touch them who wasn't Incorruptibly Pure.
Eru Ilúvatar, the ultimate Creator, left the Valar in charge of the world to guide and help the humans and Elves. When the Númenoreans decided to declare war on the Valar and invade their land, however, the Valar were unsure what to do and asked Ilúvatar to momentarily take control of the world once again. He responded by immediately sinking the Númenoreans' whole country into the sea, leaving only one ship of faithful survivors.
The Orb of Aldur in The Belgariad will kill anyone who touches it unless they are "pure", which really means "a direct descendant of its last wielder"; purity is In the Blood, apparently. As this line is thought to be extinct, and the danger is well-known, no one has touched the Orb for hundreds of years. The plot of the series kicks off when someone, somehow, manages to steal it.
In VALIS, the narrator notes that Horselover Fat's encounter with God was no better for Fat's sanity than the illegal drugs he used to take. Also, the meeting with God had the side-effect of giving cancer to all Fat's pets. (On the other hand, it's possible that the entity Fat met was not actually God—it's a point that gets debated extensively by the characters, and never completely resolved.)
C. S. Lewis has his literary avatar encounter this in Perelandra, the second book of The Space Trilogy. Lewis barely manages to fight his way past the fright tactics of harassing demons, to reach a friend's house. There, he sees a beam of unearthly light and hears an inhumanly beautiful voice speaking to him, realizes he is in the presence of an angel ... and is even more terrified. Good might rescue you from evil, but what can rescue you from good?
Live Action TV
In Supernatural, angels and demons both have to possess a human in order to walk the Earth. Angels require the consent of the human who is to be their vessel, but just because they're angels doesn't mean it's all going to turn out okay. Many angelic vessels are killed or left broken like victims of bad lobotomies after the angel is finished with them.
Mythology and Religion
This is Older Than Feudalism. In Greek Mythology seeing the undisguised glory of a god would strike mortals dead, as happened to Semele, one of Zeus' many human lovers and the mortal mother of Dionysus.
The Book of Exodus provides the page quote. Moses asks to see God's face. God answers that this would kill Moses, but He does arrange for Moses to see His back instead. Even just His back has the result of Moses' face glowing for several days and having to wear a veil in the meantime.* Funnily enough, worse translations wrote that Moses grew horns from seeing God's back, hence the presence of them on Michelangelo's sculpture of Moses.
The Ark of the Covenant was far too holy for any ordinary person to come in contact with, hence why the priests carried it with poles. Attempting to touch it, even for a good reason, as in the case of the Israelite Uzzah in 1 Samuel who tried to prevent it from falling on the ground, would result in that person being struck dead instantly. One exception is when the Ark resided in the home of Obed-Edom (right after the death of Uzzah), where the Lord blessed his household for the three months that it stayed there.
At another point in 1 Samuel (Chapters 4-7) the Israelites tried to use it as a good luck charm in battle against the Philistines. Its presence ended up galvanizing the Philistines who ripped the Israelites a new one and captured the Ark. Then the Philistines made the mistake of keeping it in the same room as an idol of Dagon, and God destroyed the statue and struck them with a plague of tumors and rats. The Philistine cities started playing hot potato with the thing and eventually decided to send it back to Israel with a guilt offering. Aaaand the Israelites promptly had a whole bunch of people die from looking into the Ark.
Judeo-Christian tradition has the archangel Metatronnote meaning "He who stands before the throne" whose job is to be the voice of God, employed any time in the Bible when people hear the voice in the sky. Presumably hearing God's voice is just as dangerous as seeing His face.
The Islamic version of the aforementioned story about Moses asking to see the face of God/Allah has it that after making a similar warning about the dangers involved, Allah told Moses that He would reveal His Face to a nearby mountain (and only that mountain), so as to let Moses witness what could happen. The result? The mountain is instantly reduced to be as even as the land around it; the implication from other Islamic traditions is that all creations of Allah cannot help but completely humble themselves before His fully unveiled glory, and that what happened to the mountain was it doing its equivalent of an extreme Pose of Supplication. As for Moses, he understandably fainted from the spectacle.
In later interpretations of Arthurian legend, the Holy Grail tended to be this. Only Sir Galahad, the purest of knights, could survive looking upon it. This might also be said to apply to the Siege Perilous, Galahad's seat at the Round Table, which marked the knight destined to complete the Grail Quest. Anyone other than Galahad who sat in it would immediately die.
In Hawaii, lava rocks and black sand are considered sacred; they are considered to be Pele's "babies." Legend has it that taking them from wherever you find them will awaken Pele's Mama Bear tendencies and bring some kind of bad luck. For this reason, many lava rocks end up being mailed back after those who took them as souvenirs attribute them to whatever misfortunes have befallen them.
The Positive Energy Plane in Dungeons & Dragons serves as the power source behind healing spells and abilities that Turn Undead, but any living being who tries to enter the plane without appropriate protection will find their bodies being overloaded with life energy and risk being vaporized if they spend too long there. Ironically, according to 3.5e Rules as Written, Undead creatures that travel to the Positive Energy Plane simply gain (temporary) hit points, and are immune to all the downsides.
From the Book of Exalted Deeds 3E sourcebook:
The Words of Creation, a precursor tongue to Celestial considered inherently good to the extent that no evil creature can speak them or bear their sound. However, most uses of the Words cause the user to suffer varying amounts of nonlethal damage (for example, speaking another creature's true name inflicts 5d4 damage on the speaker).
The same sourcebook also introduces sanctified spells, which are cross-class* As long as your character can cast spells of that level at all, you can prepare them. spells available only to good characters. Like the Words of Creation, most are Cast from Hit Points in the form of varying levels of ability damage or, in the case of Eternal Fury, death.
The White Materia, Holy, is the Planet's ultimate defensive measure. It wipes away anything it judges as a threat to the Planet, which could easily include humanity. Its only thanks to a last-minute intervention by Aerith via the Lifestream that it actually doesn't.
The various WEAPONS (giant monster creatures, not actual swords/guns/etc.) are the backup in case Holy doesn't work. Humanity is right at the top of their "to kill" list, above the Big Bad abominations actively trying to destroy the planet.
Hexen II weaponizes holiness with one of the crusader's weapons. It is a beam of holy light that burns even on the most minor of guilt that exists in all living things.
At the end of Riddle of the Sphinx, clicking on the light from the Ark of the Covenant knocks your character out temporarily.